During the same mission, Odo locates his people's homeworld in the Omarion Nebula. His joy at discovering others of his kind is short-lived, however, as the Changelings are discovered to be the Founders of the Dominion. Odo returns to DS9 with his crew mates. ("The Search, Part II")

Several Bajoran station residents leave the station out of fear of a Dominion attack. Keiko O'Brien closes the station's school after the last Bajoran student leaves. At the urging of her husband, Chief Miles O'Brien, she embarks on a six-month agrobiological expedition on Bajor. ("The House of Quark")

KaiWinn Adami and LegateTurrel begin negotiations for the Bajoran-Cardassian Treaty, with VedekBareil Antos acting as Winn's advisor. The negotiations are disrupted when Bareil is gravely injured in an accident aboard a transport ship. The location for the negotiations are moved to DS9, while Dr. Bashir takes extensive measures to save Bareil's life. Bareil guides Winn through the negotiations, leading to the signing of the treaty, however Bareil succumbs to his injuries soon after. ("Life Support")

An engineering accident caused Miles O'Brien to repeatedly shift several hours forward in time for brief intervals, during which he discovers an impending Romulan attack on both the station and the Bajoran wormhole. O'Brien dies of radiation poisoning during one of his trips forward, however the O'Brien from several hours into the alternate timeline goes back to take his place, preventing the attack. ("Visionary")

The Obsidian Order is found to be collaborating with its Romulan counterpart, the Tal Shiar, amassing numerous ships for an unsanctioned attack on the Founder homeworld. Odo and Elim Garak discover the plan and are taken prisoner. Despite having previously attempted to have Garak killed, Enabran Tain former head of the Order and architect of the plan, invites Garak to join the operation and regain his standing among his people, which Garak accepts. The operation is found to be a trap, however, as the Founder homeworld is found to be abandoned, and a fleet of 150 Jem'Hadar fighters overwhelm the Romulan and Cardassian ships in the ensuing Battle of the Omarion Nebula. Odo and Garak are the only individuals to escape, thanks to the timely arrival of the Defiant. The Obsidian Order is apparently disbanded soon after. ("Improbable Cause", "The Die is Cast")

Sisko is promoted to the rank of captain. During a subsequent mission to Tzenketh, the Defiant is sabotaged by a Changeling operative, attempting incite a war between the Federation and Tzenkethi. The crew manages to regain control of the ship, and Odo is forced to become the first Changeling to kill another of his own kind, though the dying Changeling utters an ominous warning: "You're too late. We are everywhere." ("The Adversary")

Michael Piller leaves the show to focus on creating Star Trek: Voyager, although he remains a creative consultant. Ira Steven Behr becomes the series' new Executive Producer, and effectively becomes showrunner for the remainder of the series.

At the end of season 2, the producers were alerted to the fact that feedback from the fans was not especially encouraging. In particular, young male viewers felt that DS9 didn't match up to TNG in terms of action and excitement. As well as this, many fans felt that there wasn't enough interaction with alien species and there wasn't enough traveling. Quark and Odo were the most popular characters, while Sisko was well-liked but seen as a very low-key character without much presence. Generally, episodes which dealt with religion and politics, such as "In the Hands of the Prophets" from the first season and "The Collaborator" from the second were unpopular. (Star Trek: Deep Space Nine Companion)

At the end of season 2, director of photography Marvin Rush left DS9 to begin work on VOY and was replaced by Jonathan West. West didn't bring a new lighting technique or visual style to the show, so most fans don't notice any major difference between Rush's cinematography and West's, but one thing that West did change was the type of camera lenses used. Throughout season 1 and season 2, Rush had used wide lenses which tend to separate foreground subjects from background objects by having the foreground in focus and the background out of focus and indistinct. From the start of season 3 however, West began to use telephoto lenses, which flatten the field of view between foreground and background, and as such, when characters are talking in the foreground, the station in the background is clearer to the viewer than ever seen up to this point. The producers were especially happy with this decision as they felt that it was during season 3 where characters like Sisko, Jake, and Keiko began to think of the station as their home for the first time, so it made sense that the station was now becoming more visible to the viewer. (Star Trek: Deep Space Nine Companion)